Collisional activation of protein complexes: Picking up the pieces

Critical Insight

Abstract

Mass spectrometry is fast becoming a vital approach not only for the identification and quantification of proteins, but also for the study of the noncovalent assemblies they form. Approaches for ionizing, transmitting, and detecting protein complexes intact in the mass spectrometer are now well established. The challenge has therefore shifted to developing and applying mass spectrometry approaches to elucidate the structure of such species. A crucial aspect to this goal is inducing their disassembly in the gas phase to mine information as to their composition and organization. Here the consequences of collisionally activating protein complexes are illustrated through ion mobility mass spectrometry measurements and discussed in the context of the current literature. Although a consensus view of the mechanism of dissociation is starting to emerge, it is also clear that a number of aspects remain unresolved. These outstanding questions and frontier challenges must be addressed if gas-phase dissociative approaches are to reach their full potential in the study of protein assemblies.

References

  1. 1.
    Loo, J. A. Studying Noncovalent Protein Complexes by Electrospray Ionization Mass Spectrometry. Mass Spectrom. Rev. 1997, 16, 1–23.CrossRefGoogle Scholar
  2. 2.
    Ashcroft, A. E. Recent Developments in Electrospray Ionisation Mass Spectrometry: Noncovalently Bound Protein Complexes. Nat. Prod. Rep. 2005, 22, 452–464.CrossRefGoogle Scholar
  3. 3.
    Benesch, J. L. P.; Ruotolo, B. T.; Simmons, D. A.; Robinson, C. V. Protein Complexes in the Gas Phase: Technology for Structural Genomics and Proteomics. Chem. Rev. 2007, 107, 3544–3567.CrossRefGoogle Scholar
  4. 4.
    Heck, A. J. R.; van den Heuvel, R. H. H. Investigation of Intact Protein Complexes by Mass Spectrometry. Mass Spectrom. Rev. 2004, 23, 368–389.CrossRefGoogle Scholar
  5. 5.
    Wyttenbach, T.; Bowers, M. T. Intermolecular Interactions in Biomolecular Systems Examined by Mass Spectrometry. Annu. Rev. Phys. Chem. 2007, 58, 511–533.CrossRefGoogle Scholar
  6. 6.
    Sharon, M.; Robinson, C. V. The Role of Mass Spectrometry in Structure Elucidation of Dynamic Protein Complexes. Annu. Rev. Biochem. 2007, 76, 167–193.CrossRefGoogle Scholar
  7. 7.
    McLafferty, F. W.; Fridriksson, E. K.; Horn, D. M.; Lewis, M. A.; Zubarev, R. A. Techview: Biochemistry: Biomolecule Mass Spectrometry. Science. 1999, 284, 1289–1290.CrossRefGoogle Scholar
  8. 8.
    Aebersold, R.; Mann, M. Mass Spectrometry-based Proteomics. Nature. 2003, 422, 198–207.CrossRefGoogle Scholar
  9. 9.
    Cravatt, B. F.; Simon, G. M.; Yates, J. R. 3rd The Biological Impact of Mass Spectrometry-based Proteomics. Nature 2007, 450, 991–1000.CrossRefGoogle Scholar
  10. 10.
    McConkey, E. H. Molecular Evolution, Intracellular Organization, and the Quinary Structure of Proteins. Proc. Natl. Acad. Sci. U. S. A. 1982, 79, 3236–3240.CrossRefGoogle Scholar
  11. 11.
    Domon, B.; Aebersold, R. Mass Spectrometry and Protein Analysis. Science. 2006, 312, 212–217.CrossRefGoogle Scholar
  12. 12.
    Benesch, J. L. P.; Robinson, C. V. Mass Spectrometry of Macromolecular Assemblies: Preservation and Dissociation. Curr. Opin. Struct. Biol. 2006, 16, 245–251.CrossRefGoogle Scholar
  13. 13.
    Benesch, J. L. P.; Aquilina, J. A.; Ruotolo, B. T.; Sobott, F.; Robinson, C. V. Tandem Mass Spectrometry Reveals the Quaternary Organization of Macromolecular Assemblies. Chem. Biol. 2006, 13, 597–605.CrossRefGoogle Scholar
  14. 14.
    El-Faramawy, A.; Guo, Y.; Verkerk, U.; Thomson, B. A.; Siu, M. Evaluation of IR Multi Photon Dissociation as a Method for High Mass Protein Clean Up. In 56th ASMS Conference on Mass Spectrometry, Denver, CO, 2008.Google Scholar
  15. 15.
    Felitsyn, N.; Kitova, E. N.; Klassen, J. S. Thermal Decomposition of a Gaseous Multiprotein Complex Studied by Blackbody Infrared Radiative Dissociation: Investigating the Origin of the Asymmetric Dissociation Behavior. Anal. Chem. 2001, 73, 4647–4661.CrossRefGoogle Scholar
  16. 16.
    Geels, R. B.; Calmat, S.; Heck, A. J.; van der Vies, S. M.; Heeren, R. M. Thermal Activation of the Co-Chaperonins GroES and gp31 Probed by Mass Spectrometry. Rapid Commun. Mass Spectrom. 2008, 22, 3633–3641.CrossRefGoogle Scholar
  17. 17.
    Geels, R. B.; van der Vies, S. M.; Heck, A. J.; Heeren, R. M. Electron Capture Dissociation as Structural Probe for Noncovalent Gas-Phase Protein Assemblies. Anal. Chem. 2006, 78, 7191–7196.CrossRefGoogle Scholar
  18. 18.
    Jones, C. M.; Beardsley, R. L.; Galhena, A. S.; Dagan, S.; Cheng, G.; Wysocki, V. H. Symmetrical Gas-Phase Dissociation of Noncovalent Protein Complexes via Surface Collisions. J. Am. Chem. Soc. 2006, 128, 15044–15045.CrossRefGoogle Scholar
  19. 19.
    Jennings, K. R. The Changing Impact of the Collision-induced Decomposition of Ions on Mass Spectrometry. Int. J. Mass Spectrom. 2000, 200, 479–493.CrossRefGoogle Scholar
  20. 20.
    Shukla, A. K.; Futrell, J. H. Tandem Mass Spectrometry: Dissociation of Ions by Collisional Activation. J. Mass Spectrom. 2000, 35, 1069–1090.CrossRefGoogle Scholar
  21. 21.
    Sleno, L.; Volmer, D. A. Ion Activation Methods for Tandem Mass Spectrometry. J. Mass Spectrom. 2004, 39, 1091–1112.CrossRefGoogle Scholar
  22. 22.
    Kennaway, C. K.; Benesch, J. L. P.; Gohlke, U.; Wang, L.; Robinson, C. V.; Orlova, E. V.; Saibil, H. R.; Keep, N. H. Dodecameric Structure of the Small Heat Shock Protein Acr1 from Mycobacterium Tuberculosis. J. Biol. Chem. 2005, 280, 33419–33425.CrossRefGoogle Scholar
  23. 23.
    Ruotolo, B. T.; Benesch, J. L. P.; Sandercock, A. M.; Hyung, S. J.; Robinson, C. V. Ion Mobility-Mass Spectrometry Analysis of Large Protein Complexes. Nat. Protoc. 2008, 3, 1139–1152.CrossRefGoogle Scholar
  24. 24.
    Ruotolo, B. T.; Giles, K.; Campuzano, I.; Sandercock, A. M.; Bateman, R. H.; Robinson, C. V. Evidence for Macromolecular Protein Rings in the Absence of Bulk Water. Science. 2005, 310, 1658–1661.CrossRefGoogle Scholar
  25. 25.
    Senko, M. W.; Speir, J. P.; McLafferty, F. W. Collisional Activation of Large Multiple Charged Ions Using Fourier Transform Mass Spectrometry. Anal. Chem. 1994, 66, 2801–2808.CrossRefGoogle Scholar
  26. 26.
    Smith, R. D.; Loo, J. A.; Barinaga, C. J.; Edmonds, C. G.; Udseth, H. R. Collisional Activation and Collision-Activated Dissociation of Large Multiply Charged Polypeptide and Proteins Produced by Electrospray Ionization. J. Am. Soc. Mass Spectrom. 1990, 1, 53–65.CrossRefGoogle Scholar
  27. 27.
    Sobott, F.; Robinson, C. V. Characterising Electrosprayed Biomolecules Using Tandem-MS: The Noncovalent GroEL Chaperonin Assembly. Int. J. Mass Spectrom. 2004, 236, 25–32.CrossRefGoogle Scholar
  28. 28.
    Tolić, L. P.; Bruce, J. E.; Lei, Q. P.; Anderson, G. A.; Smith, R. D. In-Trap Cleanup of Proteins from Electrospray Ionization Using Soft Sustained Off-resonance Irradiation with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem. 1998, 70, 405–408.CrossRefGoogle Scholar
  29. 29.
    Ilag, L. L.; Westblade, L. F.; Deshayes, C.; Kolb, A.; Busby, S. J.; Robinson, C. V. Mass Spectrometry of Escherichia coli RNA Polymerase: Interactions of the Core Enzyme with Sigma70 and Rsd Protein. Structure. 2004, 12, 269–275.Google Scholar
  30. 30.
    McKay, A. R.; Ruotolo, B. T.; Ilag, L. L.; Robinson, C. V. Mass Measurements of Increased Accuracy Resolve Heterogeneous Populations of Intact Ribosomes. J. Am. Chem. Soc. 2006, 128, 11433–11442.CrossRefGoogle Scholar
  31. 31.
    Hernández, H.; Robinson, C. V. Determining the Stoichiometry and Interactions of Macromolecular Assemblies from Mass Spectrometry. Nat. Protoc. 2007, 2, 715–726.CrossRefGoogle Scholar
  32. 32.
    Freeke, J.; Robinson, C. V.; Ruotolo, B. T. Residual counter ions can stabilise a large protein complex in the gas phase. Int. J. Mass Spectrom. 2008, in preparation.Google Scholar
  33. 33.
    Sun, J.; Kitova, E. N.; Klassen, J. S. Method for Stabilizing Protein-Ligand Complexes in Nanoelectrospray Ionization Mass Spectrometry. Anal. Chem. 2007, 79, 416–425.CrossRefGoogle Scholar
  34. 34.
    Steinberg, M. Z.; Elber, R.; McLafferty, F. W.; Gerber, R. B.; Breuker, K. Early Structural Evolution of Native Cytochrome c after Solvent Removal. ChemBioChem. 2008, 9, 2417–2423.CrossRefGoogle Scholar
  35. 35.
    Ruotolo, B. T.; Hyung, S. J.; Robinson, P. M.; Giles, K.; Bateman, R. H.; Robinson, C. V. Ion Mobility-Mass Spectrometry Reveals Long-lived, Unfolded Intermediates in the Dissociation of Protein Complexes: Angew. Chem. Int. Ed. Engl. 2007, 46, 8001–8004.CrossRefGoogle Scholar
  36. 36.
    Clemmer, D. E.; Hudgins, R. R.; Jarrold, M. F. Naked Protein Conformations: Cytochrome c in the Gas Phase. J. Am. Chem. Soc. 1995, 117, 10141–10142.CrossRefGoogle Scholar
  37. 37.
    Clemmer, D. E.; Jarrold, M. F. Ion Mobility Measurements and Their Applications to Clusters and Biomolecules. J. Mass Spectrom. 1997, 32, 577–598.CrossRefGoogle Scholar
  38. 38.
    Light-Wahl, K. J.; Schwartz, B. L.; Smith, R. D. Observation of the Noncovalent Quaternary Associations of Proteins be Electrospray Ionization Mass Spectrometry. J. Am. Chem. Soc. 1994, 116, 5271–5278.CrossRefGoogle Scholar
  39. 39.
    Chowdhury, S. K.; Katta, V.; Chait, B. T. Probing Conformational-Changes in Proteins By Mass-Spectrometry. J. Am. Chem. Soc. 1990, 112, 9012–9013.CrossRefGoogle Scholar
  40. 40.
    Jurchen, J. C.; Garcia, D. E.; Williams, E. R. Further Studies on the Origins of Asymmetric Charge Partitioning in Protein Homodimers. J. Am. Soc. Mass Spectrom. 2004, 15, 1408–1415.CrossRefGoogle Scholar
  41. 41.
    Jurchen, J. C.; Williams, E. R. Origin of Asymmetric Charge Partitioning in the Dissociation of Gas-Phase Protein Homodimers. J. Am. Chem. Soc. 2003, 125, 2817–2826.CrossRefGoogle Scholar
  42. 42.
    Csiszar, S.; Thachuk, M. Using Ellipsoids to Model Charge Distributions in Gas Phase Protein Complex Ion Dissociation. Can. J. Chem. 2004, 82, 1736–1744.CrossRefGoogle Scholar
  43. 43.
    Sinelnikov, I.; Kitova, E. N.; Klassen, J. S. Influence of Coulombic Repulsion on the Dissociation Pathways and Energetics of Multiprotein Complexes in the Gas Phase. J. Am. Soc. Mass Spectrom. 2007, 18, 617–631.CrossRefGoogle Scholar
  44. 44.
    Wanasundara, S. N.; Thachuk, M. Theoretical Investigations of the Dissociation of Charged Protein Complexes in the Gas Phase. J. Am. Soc. Mass Spectrom. 2007, 18, 2242–2253.CrossRefGoogle Scholar
  45. 45.
    Felitsyn, N.; Kitova, E. N.; Klassen, J. S. Thermal Dissociation of the Protein Homodimer Ecotin in the Gas Phase. J. Am. Soc. Mass Spectrom. 2002, 13, 1432–1442.CrossRefGoogle Scholar
  46. 46.
    Daggett, V.; Levitt, M. Protein Unfolding Pathways Explored through Molecular Dynamics Simulations. J. Mol. Biol. 1993, 232, 600–619.CrossRefGoogle Scholar
  47. 47.
    Aquilina, J. A. The Major Toxin from the Australian Common Brown Snake Is a Hexamer with Unusual Gas-Phase Dissociation Properties. Proteins 2008, doi:10.1002/prot.22259.Google Scholar
  48. 48.
    van den Heuvel, R. H.; van Duijn, E.; Mazon, H.; Synowsky, S. A.; Lorenzen, K.; Versluis, C.; Brouns, S. J.; Langridge, D.; van der Oost, J.; Hoyes, J.; Heck, A. J. Improving the Performance of a Quadrupole Time-of-Flight Instrument for Macromolecular Mass Spectrometry. Anal. Chem. 2006, 78, 7473–7483.CrossRefGoogle Scholar
  49. 49.
    Benesch, J. L. P.; Ruotolo, B. T.; Sobott, F.; Wildgoose, J.; Gilbert, A.; Bateman, R.; Robinson, C. V. A Q-ToF Mass Spectrometer Modified for Higher-Energy Dissociation Reduces Protein Assemblies to Peptide Fragments. Anal. Chem. 2008, in press.Google Scholar
  50. 50.
    Uetrecht, C.; Versluis, C.; Watts, N. R.; Roos, W. H.; Wuite, G. J.; Wingfield, P. T.; Steven, A. C.; Heck, A. J. High-Resolution Mass Spectrometry of Viral Assemblies: Molecular Composition and Stability of Dimorphic Hepatitis B Virus Capsids. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 9216–9220.CrossRefGoogle Scholar
  51. 51.
    Scalf, M.; Westphall, M. S.; Krause, J.; Kaufman, S. L.; Smith, L. M. Controlling Charge States of Large Ions. Science. 1999, 283, 194–197.CrossRefGoogle Scholar
  52. 52.
    Aquilina, J. A.; Benesch, J. L. P.; Bateman, O. A.; Slingsby, C.; Robinson, C. V. Polydispersity of a Mammalian Chaperone: Mass Spectrometry Reveals the Population of Oligomers in alphaB-Crystallin. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 10611–10616.CrossRefGoogle Scholar
  53. 53.
    Han, X.; Jin, M.; Breuker, K.; McLafferty, F. W. Extending Top-Down Mass Spectrometry to Proteins with Masses Greater Than 200 Kilodaltons. Science. 2006, 314, 109–112.CrossRefGoogle Scholar
  54. 54.
    Aquilina, J. A.; Benesch, J. L. P.; Ding, L. L.; Yaron, O.; Horwitz, J.; Robinson, C. V. Subunit Exchange of Polydisperse Proteins: Mass Spectrometry Reveals Consequences of alphaA-Crystallin Truncation. J. Biol. Chem. 2005, 280, 14485–14491.CrossRefGoogle Scholar
  55. 55.
    Carver, J. A.; Aquilina, J. A.; Truscott, R. J.; Ralston, G. B. Identification by 1H NMR Spectroscopy of Flexible C-Terminal Extensions in Bovine Lens alpha-Crystallin. FEBS Lett. 1992, 311, 143–149.CrossRefGoogle Scholar
  56. 56.
    Kelleher, N. L.; Lin, H. Y.; Valaskovic, G. A.; Aaserud, D. J.; Fridriksson, E. K.; McLafferty, F. W. Top Down versus Bottom Up Protein Characterization by Tandem High-Resolution Mass Spectrometry. J. Am. Chem. Soc. 1999, 121, 806–812.CrossRefGoogle Scholar
  57. 57.
    Chernushevich, I. V.; Thomson, B. A. Collisional Cooling of Large Ions in Electrospray Mass Spectrometry. Anal. Chem. 2004, 76, 1754–1760.CrossRefGoogle Scholar
  58. 58.
    Hernández, H.; Dziembowski, A.; Taverner, T.; Seraphin, B.; Robinson, C. V. Subunit Architecture of Multimeric Complexes Isolated Directly from Cells. EMBO Rep. 2006, 7, 605–610.Google Scholar
  59. 59.
    Ilag, L. L.; Videler, H.; McKay, A. R.; Sobott, F.; Fucini, P.; Nierhaus, K. H.; Robinson, C. V. Heptameric (L12)6/L10 Rather Than Canonical Pentameric Complexes Are Found by Tandem MS of Intact Ribosomes from Thermophilic Bacteria. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 8192–8197.CrossRefGoogle Scholar
  60. 60.
    Sharon, M.; Witt, S.; Felderer, K.; Rockel, B.; Baumeister, W.; Robinson, C. V. 20S Proteasomes Have the Potential to Keep Substrates in Store for Continual Degradation. J. Biol. Chem. 2006, 281, 9569–9575.CrossRefGoogle Scholar
  61. 61.
    van Duijn, E.; Simmons, D. A.; van den Heuvel, R. H.; Bakkes, P. J.; van Heerikhuizen, H.; Heeren, R. M.; Robinson, C. V.; van der Vies, S. M.; Heck, A. J. R. Tandem Mass Spectrometry of Intact GroEL-Substrate Complexes Reveals Substrate-specific Conformational Changes in the trans Ring. J. Am. Chem. Soc. 2006, 128, 4694–4702.CrossRefGoogle Scholar
  62. 62.
    Levy, E. D.; Boeri Erba, E.; Robinson, C. V.; Teichmann, S. A. Assembly Reflects Evolution of Protein Complexes. Nature. 2008, 453, 1262–1265.CrossRefGoogle Scholar
  63. 63.
    Benesch, J. L. P.; Ayoub, M.; Robinson, C. V.; Aquilina, J. A. Small Heat Shock Protein Activity Is Regulated by Variable Oligomeric Substructure. J. Biol. Chem. 2008, 283, 28513–28517.CrossRefGoogle Scholar
  64. 64.
    Wysocki, V. H.; Joyce, K. E.; Jones, C. M.; Beardsley, R. L. Surface-Induced Dissociation of Small Molecules, Peptides, and Non-Covalent Protein Complexes. J. Am. Soc. Mass Spectrom. 2008, 19, 190–208.CrossRefGoogle Scholar
  65. 65.
    Wysocki, V. H.; Jones, C. M.; Galhena, A. S.; Blackwell, A. E. Surface-Induced Dissociation Shows Potential to Be More Informative Than Collision-Induced Dissociation for Structural Studies of Large Systems. J. Am. Soc. Mass Spectrom. 2008, 19, 903–913.CrossRefGoogle Scholar
  66. 66.
    Lorenzen, K.; Versluis, C.; van Duijn, E.; van den Heuvel, R. H.; Heck, A. J. R. Optimizing Macromolecular Tandem Mass Spectrometry of Large Non-Covalent Complexes Using Heavy Collision Gases. Int. J. Mass Spectrom. 2007, 268, 198–206.CrossRefGoogle Scholar
  67. 67.
    Ackloo, S.; Chernushevich, I. V.; Loboda, A.; Haufler, R. E.; Thomson, B. A. Accessing Collision Energies of up to 500 V per Charge on a QqToF Instrument: Structure Characterization of Fullerenes and Large Peptides. In Proceedings of the 56th ASMS Conference on Mass Spectrometry, Denver, CO, 2008.Google Scholar
  68. 68.
    Sali, A.; Glaeser, R.; Earnest, T.; Baumeister, W. From Words to Literature in Structural Proteomics. Nature. 2003, 422, 216–225.CrossRefGoogle Scholar
  69. 69.
    Gingras, A. C.; Gstaiger, M.; Raught, B.; Aebersold, R. Analysis of Protein Complexes Using Mass Spectrometry. Nat. Rev. Mol. Cell. Biol. 2007, 8, 645–654.CrossRefGoogle Scholar
  70. 70.
    Heck, A. J. Native Mass Spectrometry: A Bridge between Interactomics and Structural Biology. Nat. Methods. 2008, 5, 927–933.CrossRefGoogle Scholar
  71. 71.
    Robinson, C. V.; Sali, A.; Baumeister, W. The Molecular Sociology of the Cell. Nature. 2007, 450, 973–982.CrossRefGoogle Scholar
  72. 72.
    Pringle, S. D.; Giles, K.; Wildgoose, J. L.; Williams, J. P.; Slade, S. E.; Thalassinos, K.; Bateman, R. H.; Bowers, M. T.; Scrivens, J. H. An Investigation of the Mobility Separation of Some Peptide and Protein Ions Using a New Hybrid Quadrupole/Travelling Wave IMS/oa-ToF Instrument. Int. J. Mass Spectrom. 2007, 261, 1–12.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2009

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of CambridgeCambridgeUK

Personalised recommendations